From avesani at fbk.eu Fri Aug 4 05:18:48 2023 From: avesani at fbk.eu (Paolo Avesani) Date: Fri, 4 Aug 2023 11:18:48 +0200 Subject: [Neuroimaging] Open PhD Position on Machine Learning for Brain Connectivity in Clinical Neuroscience Message-ID: OPEN PHD POSITION ON MACHINE LEARNING FOR BRAIN CONNECTIVITY IN CLINICAL NEUROSCIENCE We are pleased to announce the opening of one PhD position in neuroinformatics at the International Doctoral School in Information Engineering and Computer Science (IECS) of the University of Trento, Italy. The PhD Grant is funded by the Neuroinformatics Laboratory (NILab) of Fondazione Bruno Kessler (FBK). This project is in collaboration with the School of Medicine of the University of Trento and the Division of Neurosurgery, S. Chiara Hospital, Trento. Clinical neuroscience is playing a key role in the understanding of the brain with data of pathological alterations. The detection of anomalies in the brain structure and function is a crucial step not only for diagnosis and prognosis but also to decode the connectome of the human brain. Data driven approaches are providing promising results to characterize the patterns of the healthy brain. The challenge is to disentangle the intrinsic interindividual differences in the brain structure and function with respect to alterations related to cognitive impairment. The research objective is to investigate the most innovative techniques of Artificial Intelligence, such as geometric deep learning, to translate the knowledge of connectivity structures from a healthy population to the individual patients of a clinical study. The ultimate goal is the development of computational methods to support the detection of altered structures in the connectome affected by brain disorders. The successful candidate will have a MSc in computer science, biomedical engineering, physics, or any STEM discipline. Hands-on training in neuroimaging data analysis and/or software tools for brain connectivity will be highly valued. For reference to recent work of relevance to this project, please see (Astolfi et al., 2023), (Legarreta et al., 2021). The position is for a 3 year PhD program (Nov. 1, 2023- Oct. 31, 2026). Courses are in English. The salary is starting at approximately ?1.200/mo., net. An additional personal budget of around ?5.000 is provided for research and mobility. The University of Trento ranks among top Italian Universities (https://www.unitn.it/en/ateneo/1636/rankings). Fondazione Bruno Kessler ranks first among the Italian research centers in Engineering and Computer Science (https://magazine.fbk.eu/en/news/fbk-ranks-1st-in-italy-for-scientific-excellence-in-three-areas). Why choose Trento? (http://www.unitn.it/en/ateneo/1629/why-choose-the-university-of-trento) Important dates: Deadline for application: 5 September 2023 Beginning of PhD program: 1 November 2023 Apply now: https://iecs.unitn.it/education/admission/call-for-application (grant A7 - Deep Learning for Clinical Neuroscience) You are kindly invited to contact in advance Paolo Avesani (paolo.avesani at unitn.it). Recent related publications: - Pietro Astolfi, Ruben Verhagen, Laurent Petit, Emanuele Olivetti, Jonathan Masci, Davide Boscaini, Paolo Avesani, (2023) Supervised Tractogram Filtering Using Geometric Deep Learning", Medical Image Analysis,Volume 89. https://doi.org/10.1016/j.media.2023.102893 - Gabriele Amorosino, Denis Peruzzo, Daniela Redaelli, Emanuele Olivetti, Filippo Arrigoni, Paolo Avesani, (2022) DBB - A Distorted Brain Benchmark for Automatic Tissue Segmentation in Paediatric Patients, Neuroimage, 260. https://doi.org/10.1016/j.neuroimage.2022.119486 - Giulia Bert?, Daniel Bullock, Pietro Astolfi, Soichi Hayashi, Luca Zigiotto, Luciano Annicchiarico, Francesco Corsini, Alessandro De Benedictis, Silvio Sarubbo, Franco Pestilli, Paolo Avesani, Emanuele Olivetti, (2021) Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation", Neuroimage. https://doi.org/10.1016/j.neuroimage.2020.117402 - Paolo Avesani, Brent McPherson, Soichi Hayashi, Cesar F. Caiafa, Robert Henschel, Eleftherios Garyfallidis, Lindsey Kitchell, Daniel Bullock, Andrew Patterson, Emanuele Olivetti, Olaf Sporns, Andrew J. Saykin, Lei Wang, Ivo Dinov, David Hancock, Bradley Caron, Yiming Qian & Franco Pestilli, (2019) The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services, Nature Scientific Data, 6(69). https://doi.org/10.1038/s41597-019-0073-y -- -- Le informazioni contenute nella presente comunicazione sono di natura? privata e come tali sono da considerarsi riservate ed indirizzate? esclusivamente ai destinatari indicati e per le finalit? strettamente? legate al relativo contenuto. Se avete ricevuto questo messaggio per? errore, vi preghiamo di eliminarlo e di inviare una comunicazione? all?indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material. From sjsuss626 at gmail.com Mon Aug 14 18:11:28 2023 From: sjsuss626 at gmail.com (Stephen Suss) Date: Mon, 14 Aug 2023 18:11:28 -0400 Subject: [Neuroimaging] Reading map object as having no length Message-ID: Hello, community I have some inherent Nipype code that I edited and am running on a Linux-based operating system. I'm using Nipype version 1.8.5 and Python version 3.7. The code is crashing (error below), and understandably because Python 3 cannot read map objects as having a length. I am wondering why this error is occurring within FSL and if there is a way around it. Traceback: Traceback (most recent call last): File "/home/data/madlab/envs/emuR01_madlab_env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._run_interface(runtime) File "/home/data/madlab/envs/emuR01_madlab_env/lib/python3.7/site-packages/nipype/interfaces/fsl/model.py", line 388, in _run_interface basis_key, File "/home/data/madlab/envs/emuR01_madlab_env/lib/python3.7/site-packages/nipype/interfaces/fsl/model.py", line 218, in _create_ev_files if len(amplitudes) > 1: TypeError: object of type 'map' has no len() The above exception was the direct cause of the following exception: Traceback (most recent call last): File "emu_fsl_frstlvl_fconnect.py", line 539, in wf.run(plugin="MultiProc", plugin_args={'n_procs':40, 'overwrite': False}) File "/home/data/madlab/envs/emuR01_madlab_env/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/data/madlab/envs/emuR01_madlab_env/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 212, in run raise error from cause RuntimeError: 139 raised. Re-raising first. Best, Steve -------------- next part -------------- An HTML attachment was scrubbed... URL: From Julio.Villalon at ini.usc.edu Tue Aug 22 20:34:06 2023 From: Julio.Villalon at ini.usc.edu (Julio Villalon) Date: Wed, 23 Aug 2023 00:34:06 +0000 Subject: [Neuroimaging] Call for Papers: Methods and Applications of Diffusion MRI Tractometry Message-ID: Dear Neuroimagers, I hope this email finds you well. I am writing as the co-editor of the recently launched Research Topic, "Methods and Applications of Diffusion MRI Tractometry", published with Frontiers in Neuroscience. We are excited to bring together a comprehensive collection of cutting-edge research in the field of diffusion MRI tractometry, and we believe your knowledge and expertise could greatly contribute to the success of this endeavor. This Research Topic focuses on exploring the versatile applications of diffusion MRI tractometry in neuroscience. It seeks contributions that utilize tractometry techniques, showcase their relevance in various research fields, and highlight their use in studying brain connectivity and neurological conditions. Key areas of interest: Applications in neurological, psychiatric, and developmental disorders and in studying stroke, brain injuries, and the relationship between white matter tracts, behavior, cognitive function, and longitudinal assessments of disease progression or age-related changes in white matter connectivity. Benefits of Participation: By contributing to this research topic, your work will be published in Frontiers in Neuroscience, a reputable journal with an Impact Factor of 4.3 and a CiteScore of 6.8. This is an excellent opportunity to showcase your expertise and research findings to a wide audience in the field. Important Details: For further information about the editorial team, article types, and submission deadlines, please visit our topic's webpage: https://www.frontiersin.org/research-topics/56719. Should you have any questions or need additional clarification, please do not hesitate to contact me. Your insights and inquiries are highly valued. [https://www.frontiersin.org/files/Special%20Topics/56719/Thumb_166.jpg] Methods and Applications of Diffusion MRI Tractometry www.frontiersin.org Guest Editors: * Kurt G Schilling ??????? - Vanderbilt University Medical Center, Nashville, United States * Julio Ernesto Villal?n-Reina - University of Southern California, Los Angeles, United States * Bramsh Qamar Chandio ?? - University of Southern California, Los Angeles, United States Kind Regards, Julio Ernesto Villal?n-Reina, MD, PhD Topic Editor, Brain Imaging Methods Section, Frontiers in Neuroscience On behalf of the Topic Editors. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Wed Aug 23 09:49:09 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Wed, 23 Aug 2023 09:49:09 -0400 Subject: [Neuroimaging] [DIPY] Call for Papers: Methods and Applications of Diffusion MRI Tractometry In-Reply-To: <74234a5dca19498c972909934ca82d66@CH0PR08MB8661.namprd08.prod.outlook.com> References: <74234a5dca19498c972909934ca82d66@CH0PR08MB8661.namprd08.prod.outlook.com> Message-ID: Dear Julio, Thank you for advertising here. Such a great research topic! This is also an opportunity for me to say that tractometry is something that we really care about and have been pushing forward from 2008! When there was not even a name for this domain. We were simply calling it "along the tracts statistics (for severe tissue damage)". Lol. All sorts of technologies had to be developed here (QuickBundles, RecoBundles, BundleWarp) and in other teams around the globe to get to a stage where tractometry became useful. And now the results are often better and more robust than ever expected. A great change in the way people analyze dMRI data and hopefully a new path for future research in Neuroscience, Neurology and beyond. For those who want to submit a paper and care more about the application side of things ... You guys can simply start building on top of BUAN (our bundle analytics framework aka tractometry framework) as it is already available in DIPY. AFQ is now also an option in BUAN. Because the new AFQ uses some of BUAN's tech. Our bundle analytics framework is overall quite fast, modular and flexible. Link to our command line interfaces (CLIs) https://dipy.org/documentation/1.7.0/interfaces/buan_flow/ Link to our tutorials https://dipy.org/documentation/1.7.0/examples_built/#streamlines-analysis-and-connectivity We are also interested in building synergies with scientists/engineers who want to extend DIPY with new tractometry algorithms. Be happy to brainstorm in this thread or contact us directly. This synergy can lead to some cool advances and hopefully a paper in this special section in Frontiers. Finally, tractometry often needs access to cloud services and we have been extending DIPY to work across multiple nodes etc. If you are using BUAN in your clusters please provide feedback for improvements. We have some scripts that allow BUAN to run in ENIGMA or similar large computer networks that we can share. Happy hacking and publishing! Best regards, Elef On Tue, Aug 22, 2023 at 11:03?PM Julio Villalon wrote: > Dear Neuroimagers, > > I hope this email finds you well. I am writing as the co-editor of the > recently launched Research Topic, *"Methods and Applications of Diffusion > MRI Tractometry"*, published with * Frontiers in Neuroscience*. We are > excited to bring together a comprehensive collection of cutting-edge > research in the field of diffusion MRI tractometry, and we believe your > knowledge and expertise could greatly contribute to the success of this > endeavor. > > This Research Topic focuses on exploring the versatile applications of > diffusion MRI tractometry in neuroscience. It seeks contributions that > utilize tractometry techniques, showcase their relevance in various > research fields, and highlight their use in studying brain connectivity and > neurological conditions. > > Key areas of interest: > Applications in neurological, psychiatric, and developmental disorders and > in studying stroke, brain injuries, and the relationship between white > matter tracts, behavior, cognitive function, and longitudinal assessments > of disease progression or age-related changes in white matter connectivity. > > Benefits of Participation: > By contributing to this research topic, your work will be published in *Frontiers > in Neuroscience*, a reputable journal with an Impact Factor of 4.3 and a > CiteScore of 6.8. This is an excellent opportunity to showcase your > expertise and research findings to a wide audience in the field. > > Important Details: > For further information about the editorial team, article types, and > submission deadlines, please visit our topic's webpage: > https://www.frontiersin.org/research-topics/56719 > . > Should you have any questions or need additional clarification, please do > not hesitate to contact me. Your insights and inquiries are highly valued. > > > Methods and Applications of Diffusion MRI Tractometry > > www.frontiersin.org > > > Guest Editors: > > - Kurt G Schilling > > - Vanderbilt University Medical Center, Nashville, United States > > > - Julio Ernesto Villal?n-Reina > > - University of Southern California, Los Angeles, United States > > > - Bramsh Qamar Chandio > > - University of Southern California, Los Angeles, United States > > > Kind Regards, > > Julio Ernesto Villal?n-Reina, MD, PhD > Topic Editor, > Brain Imaging Methods Section, Frontiers in Neuroscience > On behalf of the Topic Editors. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Tue Aug 29 13:11:09 2023 From: matthew.brett at gmail.com (Matthew Brett) Date: Tue, 29 Aug 2023 18:11:09 +0100 Subject: [Neuroimaging] Discourse discussions ported to Github Discussions Message-ID: Hi, Sorry for the inconvenience, but Discourse has very reasonably closed down our nipy.discourse.group site because we were not using it. Rather than re-open the site, I've moved all the content to Github discussions. So, you'll find all previous discussion of: * Neuroimaging data formats at https://github.com/orgs/open-dicom/discussions/categories/neuroimaging-data-formats * DICOM conversion at https://github.com/orgs/open-dicom/discussions/categories/dicom * Surface API at https://github.com/orgs/nipy/discussions/categories/surface-api This also means that I've enabled Github discussions for the Nipy organization, and the Open-DICOM organization. If you spot anything missing or incorrect - please either edit, or let me know. Cheers, Matthew